The Experts below are selected from a list of 324 Experts worldwide ranked by ideXlab platform
Ruey-hwang Chou - One of the best experts on this subject based on the ideXlab platform.
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S100A4 inhibits cell proliferation by interfering with the S100A1-RAGE V domain - Fig 1
2019Co-Authors: Md. Imran Khan, Tai Yuan, Ruey-hwang ChouAbstract:(A) Superimposed HSQC of the 15N S100A4 complex with unlabeled S100A1 (red) and free 15N S100A4 (black). Peaks indicating reduced intensity appear in green boxes. (B) Ribbon Diagram showing the structure of S100A4; intensity decreasing residues are labeled on the structure in cyan.
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S100A4 inhibits cell proliferation by interfering with the S100A1-RAGE V domain - Fig 2
2019Co-Authors: Md. Imran Khan, Tai Yuan, Ruey-hwang ChouAbstract:(A) Overlapping 15N S100A1 HSQC spectra (black) and the 15N S100A1 complex with unlabeled S100A4 (red). The cross peaks, which exhibited decreased intensity, are boxed in green. (B) Ribbon Diagram showing the structure of S100A1—decreasing residues are labeled on the structure in green.
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 5
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled lysozyme (red) and of 15N-labeled lysozyme with unlabeled tranilast (blue). Disappearing cross peak intensities are boxed in green. (B) The 3D Ribbon Diagram of lysozyme (red) shows the identified interacting residues to tranilast as sticks (cyan).
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 2
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled mS100A6 (red) and of 15N-labeled mS100A6 with unlabeled lysozyme (blue). Disappearing cross peak intensities which represent interacting amino acids (G10, F16, H27, R62, E72, Y73, F76 and G78) are boxed in green. (B) The 3D Ribbon Diagram of the monomer mS100A6 (blue) shows residues interacting with lysozyme in sticks form (green).
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 1
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled lysozyme (red) and of 15N-labeled lysozyme with mS100A6 (blue). Disappearing cross peak intensities which represent interacting amino acids (V2, R5, N37, T47, D48, T51, G54, S60, N65, S81 and S86) are boxed in green. (B) The 3D Ribbon Diagram of lysozyme (red) shows residues interacting with mS100A6) in sticks form (cyan).
Marcy H Towns - One of the best experts on this subject based on the ideXlab platform.
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students understanding of external representations of the potassium ion channel protein part ii structure function relationships and fragmented knowledge
Biochemistry and Molecular Biology Education, 2012Co-Authors: Marissa Harle, Marcy H TownsAbstract:Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This study focuses on students' understanding of three external representations (Ribbon Diagram, wireframe, and hydrophobic/hydrophilic) of the potassium ion channel protein. Analysis of the interview data demonstrates that students were able to use the Ribbon structures and polarity of the cell membrane to help support claims about the protein's orientation and interactions within the cell membrane. Students expressed fragmented understandings of the interactions between the potassium ion and the aqueous solution outside/inside of the cell membrane. Suggestions for instruction are to probe student understanding to help students activate prior knowledge and to help them build a more connected set of concepts pertaining to protein structure and function.
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Students' understanding of external representations of the potassium ion channel protein, part I: Affordances and limitations of Ribbon Diagrams, vines, and hydrophobic/polar representations†
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 2012Co-Authors: Marissa Harle, Marcy H TownsAbstract:Research on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This project focuses on students' understanding of three external representations of the potassium ion channel protein. This is part I of a two-part study, which focuses on the affordances and limitations of representations of the potassium ion channel according to students across the chemistry and biochemistry curriculum. Analysis showed that if the students do not possess the required prior knowledge then they are stymied in their interpretations of the representations. Students were able to easily interpret the familiar Ribbon Diagram representation; however, they found the vines and hydrophobic/polar representations to be less informative. Suggestions for instruction are to probe student understanding and to help students activate prior knowledge to build a more connected set of concepts pertaining to protein structure.
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Students' understanding of external representations of the potassium ion channel protein part II: Structure–function relationships and fragmented knowledge
Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology, 2012Co-Authors: Marissa Harle, Marcy H TownsAbstract:Research that has focused on external representations in biochemistry has uncovered student difficulties in comprehending and interpreting external representations. This study focuses on students' understanding of three external representations (Ribbon Diagram, wireframe, and hydrophobic/hydrophilic) of the potassium ion channel protein. Analysis of the interview data demonstrates that students were able to use the Ribbon structures and polarity of the cell membrane to help support claims about the protein's orientation and interactions within the cell membrane. Students expressed fragmented understandings of the interactions between the potassium ion and the aqueous solution outside/inside of the cell membrane. Suggestions for instruction are to probe student understanding to help students activate prior knowledge and to help them build a more connected set of concepts pertaining to protein structure and function.
Jeffrey C Boyington - One of the best experts on this subject based on the ideXlab platform.
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Overview of protein structural and functional folds.
Current protocols in protein science, 2004Co-Authors: Peter D Sun, Christine E Foster, Jeffrey C BoyingtonAbstract:This overview provides an illustrated, comprehensive survey of some commonly observed protein-fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web-based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein-structure databases, protein-structure-classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including Ribbon-Diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
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Current Protocols in Protein Science - Overview of protein structural and functional folds.
Current Protocols in Protein Science, 2004Co-Authors: Peter D Sun, Christine E Foster, Jeffrey C BoyingtonAbstract:This overview provides an illustrated, comprehensive survey of some commonly observed protein-fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web-based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein-structure databases, protein-structure-classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including Ribbon-Diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
Md. Imran Khan - One of the best experts on this subject based on the ideXlab platform.
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S100A4 inhibits cell proliferation by interfering with the S100A1-RAGE V domain - Fig 1
2019Co-Authors: Md. Imran Khan, Tai Yuan, Ruey-hwang ChouAbstract:(A) Superimposed HSQC of the 15N S100A4 complex with unlabeled S100A1 (red) and free 15N S100A4 (black). Peaks indicating reduced intensity appear in green boxes. (B) Ribbon Diagram showing the structure of S100A4; intensity decreasing residues are labeled on the structure in cyan.
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S100A4 inhibits cell proliferation by interfering with the S100A1-RAGE V domain - Fig 2
2019Co-Authors: Md. Imran Khan, Tai Yuan, Ruey-hwang ChouAbstract:(A) Overlapping 15N S100A1 HSQC spectra (black) and the 15N S100A1 complex with unlabeled S100A4 (red). The cross peaks, which exhibited decreased intensity, are boxed in green. (B) Ribbon Diagram showing the structure of S100A1—decreasing residues are labeled on the structure in green.
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 5
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled lysozyme (red) and of 15N-labeled lysozyme with unlabeled tranilast (blue). Disappearing cross peak intensities are boxed in green. (B) The 3D Ribbon Diagram of lysozyme (red) shows the identified interacting residues to tranilast as sticks (cyan).
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 2
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled mS100A6 (red) and of 15N-labeled mS100A6 with unlabeled lysozyme (blue). Disappearing cross peak intensities which represent interacting amino acids (G10, F16, H27, R62, E72, Y73, F76 and G78) are boxed in green. (B) The 3D Ribbon Diagram of the monomer mS100A6 (blue) shows residues interacting with lysozyme in sticks form (green).
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Lysozyme as the anti-proliferative agent to block the interaction between S100A6 and the RAGE V domain - Fig 1
2019Co-Authors: Md. Imran Khan, Ruey-hwang Chou, Deepu Dowarha, Revansiddha Katte, Anna FilipekAbstract:(A) Overlapped HSQC spectra of 15N-labeled lysozyme (red) and of 15N-labeled lysozyme with mS100A6 (blue). Disappearing cross peak intensities which represent interacting amino acids (V2, R5, N37, T47, D48, T51, G54, S60, N65, S81 and S86) are boxed in green. (B) The 3D Ribbon Diagram of lysozyme (red) shows residues interacting with mS100A6) in sticks form (cyan).
Richard Charles Garratt - One of the best experts on this subject based on the ideXlab platform.
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The reconstruction of atomic co-ordinates from a protein stereo Ribbon Diagram when additional information for sufficient sidechain positions is available.
Journal of computer-aided molecular design, 1998Co-Authors: Paulo Sérgio Lopes De Oliveira, Richard Charles GarrattAbstract:We describe the application of a method for the reconstruction of three-dimensional atomic co-ordinates from a stereo Ribbon Diagram of a protein when additional information for some of the sidechain positions is available. The method has applications in cases where the 3D co-ordinates have not been made available by any means other than the original publication and are of interest as models for molecular replacement, homology modelling etc. The approach is, on the one hand, more general than other methods which are based on stereo figures which present specific atomic positions, but on the other hand relies on input from a specialist. Its exact implementation will depend on the figure of interest. We have applied the method to the case of the α-d-galactose-binding lectin jacalin with a resultant RMS deviation, compared to the crystal structure, of 1.5 A for the 133 Cα positions of the α-chain and 2.6 A for the less regular β-chain. The success of the method depends on the secondary structure of the protein under consideration and the orientation of the stereo Diagram itself but can be expected to reproduce the mainchain co-ordinates more accurately than the sidechains. Some ways in which the method may be generalised to other cases are discussed.